The applications listed here are available for use in the Discovery Environment and are documented in: Discovery Environment Manual.

Discovery Environment Applications List

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Tassel4 Conversion (USER MANUAL UNDER DEVELOPMENT)

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This application harnesses the conversion capabilities of the Tassel 3 pipeline in order to facilitate conversion of common GWAS file formats.

Quick Start

  • Select the expandable menu that matches your input file format. 
  • Upload all required input files within that menu. 
  • Select the Output expandable menu (it will be the last expandable menu option).
  • Select the file-format that matches the format you would like to export to from the drop-down list. 
  • Launch analysis. Once the conversion is completed the converted file will be found within the relevant analysis subfolder with the same name as your input file but with the converted format extension.
  • Resources: http://www.maizegenetics.net/tassel/docs/TasselPipelineCLI.pdf

Test Data

Icon

Test data for this app appears directly in the Discovery Environment in the Data window under Community Data -> iplantcollaborative -> example_data -> Tassel3 Conversion.

Available Input Formats

Format

Extension(s)

HapMap

.hmp.txt

Flapjack

.map, .geno

FASTA

.fas

Genetic Map

.map, .txt

HDF5

.hdf5

VCF

.vcf

Available Export Formats

Format

Extension(s)

HapMap

.hmp.txt

HapMap Diploid

.hmp.txt

HDF5

..hdf5

VCF

.vcf

Flapjack

.map, .geno

Phylip (Sequential)

.phy or .ph

Phylip (Interleaved)

.phy or .ph

Tab Delimited Text

.txt

Tool Source for App

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